that transmissions were not independent in the DZ families due to the presence of linkage in DZ pairs, a permutation procedure (10,000 permutations) was used to correct the p-values for the orthogonal test. Secondly, analyses of all 2618 families were performed using a test of total association which considers transmissions between and within families. For the test of total association, families with either one twin or two MZ twins only contribute to the ‘between’ component and a simple permutation procedure can not be applied. Thus, non-independent transmissions were corrected for by modeling linkage and association within a maximum likelihood framework. MZ twin status was included in QTDT analyses by adding zygosity status to the data file. Thirdly, quantitative haplotypic association was tested in the QPDTPHASE module of the UNPHASED statistical package (Dudbridge, 2003) which only allows analysis of the ‘within’ component in DZ families. To reduce multiple testing, haplotype testing was only performed on four alcohol-related traits of interest (factAD3r_1, factAD4, sumAbuse, sumAD3r).
